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1 <tool id="plot_adjacency" name="Plot Adjacency Matrix">
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2 <description></description>
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3 <command interpreter="python">plot_adjacency.py $node_attr $edges $Adjacency \$INSTALL_RUN_PATH/</command>
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4 <requirements>
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5 <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
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6 </requirements>
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7 <inputs>
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8 <param format="tabular" name="node_attr" type="data" label="Node Attribute File"/>
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9 <param type="sif" name="edges" type = data label="Network File"/>
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10 </inputs>
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11 <outputs>
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12 <data format="html" name="Adjacency" label="Adjacency Matrix"/>
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13 </outputs>
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14 <stdio>
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15 <regex match="Error|error"
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16 source="stdout"
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17 level="fatal"
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18 description="Unknown error"/>
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19 <regex match="Error|error"
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20 source="stderr"
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21 level="fatal"
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22 description="Unknown error"/>
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23 </stdio>
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24
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25 <tests>
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26 <test>
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27 <param name="input" value="fa_gc_content_input.fa"/>
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28 <output name="out_file1" file="fa_gc_content_output.txt"/>
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29 </test>
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30 </tests>
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31 <help>
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32 Plot Adjacency Matrix
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33 ----------------------------------------
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34
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35 This tool reads in a network SIF file and it's corresponding node attributes
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36 and plots an interactive adjacency matrix in HMTL format
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37
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38 **1) Node Attributes File **
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39 This file must be output from Network Attributes Tool of the network
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40 file being input below.
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41
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42 **2) Network File**
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43
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44 Please input a network SIF file matching the Node Attribute file above
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45 </help>
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46 </tool>
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